Brownian motion alone may not be sufficient to supply ribosomes with tRNA during translation elongation
ORAL
Abstract
The construction of artificial cells holds significant promise for biotechnology and medicine. However, substantial work remains to make such cells modelable. In particular, the set of functions necessary for life remains elusive, most acutely demonstrated by the existence of genes of unknown function that are essential for life1.
We hypothesize that some of the functions that remain unknown pertain to the physics of how molecules organize to produce cellular functions. To test our hypothesis we introduce translation elongation in E. coli as a model system. Due to its central role in protein production, elongation is likely to have undergone tremendous selective pressure to operate at the limits of physics. We construct a colloidal model of elongation and demonstrate that variable local volume densities around ribosomes at different growth rates may lead to competing trade-offs in tRNA transport and reaction. We then use lower-bounding simulations to show that tRNA transport via Brownian motion alone may be insufficient to recover experimentally determined elongation rates. Overall, we predict that currently unknown mechanisms for speeding up tRNA transport or biasing its spatial organization are implicated in translation elongation.
1Maheshwari et al. Phys. Rev. Fluids (2019)
We hypothesize that some of the functions that remain unknown pertain to the physics of how molecules organize to produce cellular functions. To test our hypothesis we introduce translation elongation in E. coli as a model system. Due to its central role in protein production, elongation is likely to have undergone tremendous selective pressure to operate at the limits of physics. We construct a colloidal model of elongation and demonstrate that variable local volume densities around ribosomes at different growth rates may lead to competing trade-offs in tRNA transport and reaction. We then use lower-bounding simulations to show that tRNA transport via Brownian motion alone may be insufficient to recover experimentally determined elongation rates. Overall, we predict that currently unknown mechanisms for speeding up tRNA transport or biasing its spatial organization are implicated in translation elongation.
1Maheshwari et al. Phys. Rev. Fluids (2019)
–
Presenters
-
Akshay J Maheshwari
Bioengineering, Stanford University, Stanford Univ
Authors
-
Akshay J Maheshwari
Bioengineering, Stanford University, Stanford Univ
-
Emma del Carmen Gonzalez Gonzalez
Chemical Engineering, Stanford University, Stanford Univ
-
Alp M Sunol
Chemical Engineering, Stanford University, Stanford Univ, Department of Chemical Engineering, Stanford University
-
Drew Endy
Bioengineering, Stanford University, Stanford Univ
-
Roseanna Zia
Chemical Engineering, Stanford University, Department of Chemical Engineering, Stanford University, Stanford Univ